BMRB Entry 25437

Name: Endo T5-ZN+2
Published: 2015-02-09

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PDB ID: 2mxz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25437
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Endo T5-ZN+2

Deposition date:

2015-01-19

Original release date:

2015-02-09

Authors:

Prokhorov, Dmitry; Mikoulinskaia, Galina; Molochkov, Nikolai; Kutyshenko, Victor

Citation:

Citation: Kutyshenko, Victor; Mikoulinskaia, Galina; Molochkov, Nikolai; Prokhorov, Dmitry; Taran, Sergei; Uversky, Vladimir. "Structure and dynamics of the retro-form of the bacteriophage T5 endolysin" Biochim. Biophys. Acta 1864, 1281-1291 (2016).
PubMed: 27376687

Assembly members:

Assembly members:
l-alanoyl-d-glutamate_peptidase, polymer, 137 residues, 15286.351 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: Bacteriophage T5 Taxonomy ID: 10726 Superkingdom: Viruses Kingdom: not available Genus/species: T5likevirus Enterobacteria phage T5

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET3a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
l-alanoyl-d-glutamate_peptidase: MSFKFGKNSEKQLATVKPEL QKVARRALELSPYDFTIVQG IRTVAQSAQNIANGTSFLKD PSKSKHITGDAIDFAPYING KIDWNDLEAFWAVKKAFEQA GKELGIKLRFGADWNASGDY HDEIKRGTYDGGHVELV

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	475
15N chemical shifts	135
1H chemical shifts	932

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	l-alanoyl-d-glutamate_peptidase	1
2	ZINC ION	2

Entities:

Entity 1, l-alanoyl-d-glutamate_peptidase 137 residues - 15286.351 Da.

1

MET

SER

PHE

LYS

PHE

GLY

LYS

ASN

SER

GLU

2

LYS

GLN

LEU

ALA

THR

VAL

LYS

PRO

GLU

LEU

3

GLN

LYS

VAL

ALA

ARG

ALA

LEU

GLU

LEU

4

SER

PRO

TYR

ASP

PHE

THR

ILE

VAL

GLN

GLY

5

ILE

ARG

THR

VAL

ALA

GLN

SER

ALA

GLN

ASN

6

ILE

ALA

ASN

GLY

THR

SER

PHE

LEU

LYS

ASP

7

PRO

SER

LYS

SER

LYS

HIS

ILE

THR

GLY

ASP

8

ALA

ILE

ASP

PHE

ALA

PRO

TYR

ILE

ASN

GLY

9

LYS

ILE

ASP

TRP

ASN

ASP

LEU

GLU

ALA

PHE

10

TRP

ALA

VAL

LYS

ALA

PHE

GLU

GLN

ALA

11

GLY

LYS

GLU

LEU

GLY

ILE

LYS

LEU

ARG

PHE

12

GLY

ALA

ASP

TRP

ASN

ALA

SER

GLY

ASP

TYR

13

HIS

ASP

GLU

ILE

LYS

ARG

GLY

THR

TYR

ASP

14

GLY

HIS

VAL

GLU

LEU

VAL

Entity 2, ZINC ION - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: l-alanoyl-d-glutamate peptidase, [U-100% 13C; U-100% 15N], 0.8 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.05 M; pH: 4.1; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Bruker Avance III 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks